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    Kang Jin

    Kang.Jin at cchmc.org [Github] [Google Scholar] [Twitter]
    Last updated: 09/25/2023

    Research Interest

    Hi, I am a fifth-year Ph.D. student in Biomedical Informatics Division under the supervision of Dr. Bruce Aronow at Cincinnati Children’s Hospital. I am currently visiting Shu lab at Massachusetts General Hospital, where I am learning spatial transcriptomics technologies.

    As an enthusiastic researcher, I am passionate about harnessing advanced computational techniques to unveil the biological mechanisms hidden within high-throughput sequencing and high-content imaging data, with a specific focus on image-based spatial profiling. My present work primarily centers around the development of cutting-edge deep learning models tailored to image-based spatial omics data (Jin*, Zhang* et al., bioRxiv, 2023) and the analysis of temporal perturbation patterns in single-cell experiments (Jin et al., Briefings in Bioinformatics, 2022). My commitment extends to active involvement in the experimental design of spatial multi-omics experiments, and I possess a wealth of experience in exploring single cell data across various biological systems and diseases, including HLHS (Xu, Jin et al., Cell Stem Cell, 2022), schizophrenia (Sebastian*, Jin* et al. Nat Communications, 2023), among others.

    I am particularly interested in cutting-edge bioengineering innovations, such as image-based spatial transcriptomics and optical molecular recording. Collaborating with Dr. Jian Shu, we are devotedly developing innovative methods for in-situ molecular recording through microscopy.

    With expertise in computational biology and a strong interest in bioengineering, my ultimate goal is to advance our understanding of neuroscience and cancer biology by implementing cutting-edge computational methods with emerging new molecular recording technologies.

    Position & Education

    2022 - Present, Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School,

    Visiting student

    2018 - Present, Department of Biomedical Informatics, Cincinnati Children's Hospital, University of Cincinnati,

    Ph.D. student

    2014 - 2018, Department of Life Sciences, Zhejiang University,

    Bachelor of Biological Science

    Publications

    (*Equal contribution)
    Published papers (as main author)

    • Bering: joint cell segmentation and annotation for spatial transcriptomics with transferred graph embeddings [paper] [code]
      Kang Jin*, Zuobai Zhang*, Ke Zhang, Francesca Viggiani, Claire Callahan, Jian Tang, Bruce J. Aronow, Jian Shu
      bioRxiv (2023).

    • CellDrift: Inferring Perturbation Responses in Temporally-Sampled Single Cell Data [paper] [code]
      Kang Jin, Dan Schnell, Guangyuan Li, Nathan Salomonis, Surya Prasath, Rhonda Szczesniak, Bruce J Aronow
      Briefings in Bioinformatics (2022).

    • Single cell transcriptomic profiling of human brain organoids reveals developmental timing- and cell-type-specific vulnerabilities induced by NRXN1 CNVs in schizophrenia [paper] [code]
      Rebecca Sebastian*, Kang Jin*, Narciso Pavon, Ruby Bansal, Andrew Potter, Yoonjae Song, Juliana Babu, Rafael Gabriel, Yubing Sun, Bruce Aronow, ChangHui Pak
      Nature Communications (2023).

    • An interactive single cell web portal identifies gene and cell networks in COVID-19 host responses [paper] [code]
      Kang Jin, Eric E. Bardes, Alexis Mitelpunkt, Jake Y. Wang, Surbhi Bhatnagar, Soma Sengupta, Daniel Pomeranz Krummel, Marc E. Rothenberg, Bruce J. Aronow
      iScience (2021).

    • Uncompensated mitochondrial oxidative stress underlies heart failure in an iPSC-derived model of congenital heart disease [paper]
      Xinxiu Xu, Kang Jin, Abha S Bais, Wenjuan Zhu, Hisato Yagi, Timothy N Feinstein, Phong K Nguyen, Joseph D Criscione, Xiaoqin Liu, Gisela Beutner, Kalyani B Karunakaran, Krithika S Rao, Haoting He, Phillip Adams, Catherine K Kuo, Dennis Kostka, Gloria S Pryhuber, Sruti Shiva, Madhavi K Ganapathiraju, George A Porter Jr, Jiuann-Huey Ivy Lin, Bruce Aronow, Cecilia W Lo
      Cell Stem Cell (2022).

    • Identification of distinct tumor cell populations and key genetic mechanisms through single cell sequencing in hepatoblastoma [paper] [code]
      Alexander Bondoc*, Kathryn Glaser*, Kang Jin*, Charissa Lake, Stefano Cairo, James Geller, Gregory Tiao, Bruce Aronow
      Communications Biology (2021).

    Published papers (as contributing author)

    • Guided construction of single cell reference for human and mouse lung [paper]
      Minzhe Guo, Michael P Morley, Yixin Wu, Yina Du, Shuyang Zhao, Andrew Wagner, Michal Kouril, Kang Jin, ..., Yan Xu
      Nature Communications (2023).

    • KAT5 activity regulates G0-like states in human gliomas [paper]
      Anca B. Mihalas, Sonali Arora, Samantha A. O’Connor, Heather M. Feldman, John Bassett, Kelly Mitchell, Kang Jin, ..., Patrick J. Paddisons
      bioRxiv (2022).

    • LungMAP Portal Ecosystem: Systems-Level Exploration of the Lung [paper]
      Nathan Gaddis, Joshua Fortriede, Minzhe Guo, ..., Kang Jin, ..., Nathan Salomonis, NHLBI LungMAP Consortium
      American Journal of Respiratory Cell and Molecular Biology (2022).

    • Loss of Neurodevelopmental Gene CASK Disrupts Neural Connectivity in Human Cortical Excitatory Neurons [paper]
      Danny McSweeney, Rafael Gabriel, Kang Jin, Zhiping P Pang, Bruce J Aronow, ChangHui Pak
      iScience (2022).

    • A census of the lung: CellCards from LungMAP [paper]
      Xin Sun, Anne-Karina Perl, Rongbo Li, ..., Kang Jin, ..., Edward E Morrisey, NHLBI LungMAP Consortium
      Developmental Cell (2022).

    • Cross-platform validation of neurotransmitter release impairments in schizophrenia patient-derived NRXN1-mutant neurons [paper]
      ChangHui Pak, Tamas Danko, Vincent R. Mirabella, Jinzhao Wang, Yingfei Liu, Madhuri Vangipuram, Sarah Grieder, Xianglong Zhang, Thomas Ward, Yu-Wen Alvin Huang, Kang Jin, ..., Thomas C. Südhof
      PNAS (2021).

    • Functional immune deficiency syndrome via intestinal infection in COVID-19 [paper]
      Erica T. Prates, Michael R. Garvin, Mirko Pavicic, Piet Jones, Manesh Shah, Christiane Alvarez, David Kainer, Omar Demerdash, B Kirtley Amos, Armin Geiger, John Pestian, Kang Jin, Alexis Mitelpunkt, Eric Bardes, Bruce Aronow, Daniel Jacobson
      bioRxiv (2020).

    • Predicted Arabidopsis interactome resource and gene set linkage analysis: a transcriptomic analysis resource [paper]
      Heng Yao, Xiaoxuan Wang, Pengcheng Chen, Ling Hai, Kang Jin, Lixia Yao, Chuanzao Mao, Xin Chen
      Plant Physiology (2018).

    Softwares

    • Bering: Cell segmentation and annotation in high-resolution spatial transcriptomics data

    • ToppCell: Single-cell gene module exploratory platform

    • CellDrift: Inferring Perturbation Responses in Temporally-Sampled Single Cell Data.

    • Bering: Gene colocalization-aware segmentation of image-based spatial transcriptomics using deep learning models (Wrapping up)

    Resources

    Honors and Awards

    • Second Place, Best Poster Award, ISMB 2022 (SysMod Meeting) 2022
    • Second Place in Graduate Student Research Forum (GSRF), University of Cincinnati, 2020
    • Best Application Award of Zhejiang Bioinformatics Competition,2017
    • China National Award, 2017
    • First Prize Scholarship for Excellent Students, Zhejiang University, 2017
    • Tang Lixin Scholarship for Excellent Model Student, 2017
    • Zhejiang Provincial Government Scholarship, 2016
    • Second Prize, Physics Innovation Competition in Zhejiang Province, 2015